Issues of Omniscience
by noctisxsol
Summary: After one hundred thousand years of living as the consciousness of the Reapers, Shepherd awakens to discover that it was all a vision of the future from the Eden Prime Beacon. Filled with more knowledge and skills than even he should be allowed to have, Commander stumbles out to save the Galaxy. Now if only he knew when he was... Crack.
1. A Foreward with a Long Title

**Issues of Omniscience**

 **Disclaimer: I don't own Mass Effect, and am not making money off of these stories.**

 **That said, the world these hypothetical train-wreaks of a story take place in is AU, and anyone expecting sanity or canon should flee far away. The idea for these stories came from playing Mass Effect 3, and my realization that EA didn't lay on the Messianic overtones nearly enough. To correct this, I have decided to make this series of barely connected stories based on a universe where Shepard gains near omniscience from using the Beacons.**

 **Chapter O/1 is the introduction written in the style of a bad preface to an utterly generic history textbook. If that is not your thing, move on to the actual madness.**

 **Text key**

"speaking" _"thinking"_ **"Reaper speaking"** -Scene info-

-Chapter 0; The Only Possible Genuine and Absolutely Trustworthy and Non-Contradictory History of Commander Shepard, and How he Came to be Remembered as he is Today-

-A History with an Over-Long Title-

Written in Liquid Sincerity By Noctis Sol

There are few historical figures that are more inspiring, but less clear than Commander Shepard. Almost any school-child will be able to tell you the generics of his greatest deeds, but most of the details are either unclear, or contradicted. This has gotten to the point where it seems that no one knows his given first name, or if he was actually a he or if Shepard was actually a female. Many Post-Post-Post-Modern Historians dismissed him as nothing more than a fictional character akin to the ancient legends of Hercules, Aladdin, or Donald Trump. This is of course preposterous, as the ample amount of historical records, inscribed monuments, and memes attest. Thus, the Author has undertaken the effort to write the first Post-Post-Post-Post Modern History which will obviously please everyone and stand until the end of time as the definitive history of Commander Shepard.

Before any more progress is made, the question of Shepard's gender must be answered. As astute readers can tell, the Author maintains the view that Shepard was male. There have been an astounding number of occurrences of confused gender in the past, both fictional (The infamous Bishonnen Link debacle of 2023 bears this out1) and Historical (It seems that half of society believes that the president Clinton who was the second American president to be impeached was a Woman. That is absurd. That president Clinton was the third2). However, this instance of gender confusion is caused primarily by a translation mishap, rather than ignorance. Most students learned about the deeds of the commander through reading the Portland University translation of Liara's records, since the alliance lost their information on Shepard during the 7-Zetabyte incident. The reason that Liara's record is significant is that it was written in her native Asari dialect, as well as Portland University's wooden translation policy.

The problem begins with specific dialect in which Liara wrote her record. Most Asari dialects have adapted their pronoun system to be fully bi-gendered; however, the Pureblood Dialect is partially-gendered. What that means is that while male and female pronouns do exist, they are not used for people, only animals. Thus, whenever she referenced someone for whom she held high respect, she would use a pronoun that is considered feminine. While an in-depth study would easily parse out this minor miscommunication, the overworked TAs at Portland University did not have that time. As an Alumnus of PU I must be the first to admit that their translations stink, and that they should really change their name around. The translation issue was only made worse by the Portland Blackout Rebellion, which spanned the course of the writing and cut off the translators from outside sources. While the minor issue would normally have been corrected by Citadel Fact Checkers, it just so happened that the checkers for this work included a belligerent Radical Feminist. The rest is probably best explained by the sharp rise in hospitalizations for omni-blade castrations.

That is not to say that The Author believes a woman to be incapable of the feats that Shepard accomplished, it's just that Shepard's N-7 armor contains a cod-piece and a distinct lack of breasts.

Now that Shepard's gender is solved, his history can be unraveled. Contrary to popular belief, Shepard's first name is actually well know, and said by nearly everyone who speaks of him. He was born Commander Shepard to James and Hannah Shepard, two individuals who nearly deserve books unto themselves. James Tiberius Shepard was the son of Kirk Shepard, the famous general who negotiated the peace for the First Contact War and also the one who invented Fornax. The mother is unknown but rumors at the time assert that the mother was a Krogan War Mistress that he defeated in hand-to-hand. James himself was famed for being the first non-Krogan to train on Tuchanka, as well as killing a Thresher Maw on foot. Hannah Ripley Smith Shepard was famous for being the first human to beat a Turian team at War Games, and the only one to do so single-handedly. She was the one who chose the strange name for her son.

Near the time of Commander's birth, a Volus ship crash-landed on earth, and the suits of three of the crew were ruptured. Since the integration of translators and the extranet were still ongoing at that time, the Volus were left asking desperately for skilled assistance using the job titles Smith and Tailor. Those were common Earth names, and misunderstandings led to the first responders thinking they were looking for people by the name of Smith or Taylor. Due to the confusion, the three Volus died, and the Alliance Politicians made a bill that, had it passed, would have required everyone with a name that was also a profession to legally change their name. Understandably, both James Shepard and Hannah Smith would have been affected. The bill took nearly a decade to be dismissed, but Commander was born during that time, and given his strange name as a small dig against the meddling pencil pushers.

Unfortunately, one of the nurses thought that the strange name was a sign of poor parenting and kidnapped the child, leaving him in an orphanage. Commander would spend the first eight years of his life in that orphanage, learning the shadier side of the world from the older children in the orphanage. On his eighth birthday was the first and only time he got caught stealing. Coincidentally, it just so happened to be by his uncle, who adopted him and brought him out to live in the colonies. For three years Commander lived as the adopted child of his aunt and uncle Beru and Owen. It was on his Eleventh birthday that the Batarians attacked Mindor, killed his aunt and Uncle, as well as the first time that Shepard used a gun. Good came out of the attack though, as his mother found him when she was sent to help the colony. Shepard finally re-united with his parents, and joined the Alliance where the brass accidentally thought that his name was his rank and assigned the new commander to Elysium, where there would at least be back-up. In a strange twist of fate, the "new guy" saved the colony and became a hero, but refused promotion to "Screw with everyone's' heads."

Commander's next assignment was the tragedy at Akuze. The Alliance forces were lured into a thresher nest with a false distress beacon. Almost everyone died. Shepard lived up to his parents' legacies by managing to force the Thresher maws to retreat, but it seemed that he was the only survivor. It was soon after Akuze that Shepard left for N-7 training. Not long after his return, he was assigned to the new experimental ship Normandy SR-1. His first mission aboard the ship was when everything changed, and history was remade in his image…

 **For those of you who aren't Americans/ are Americans but are ignorant of either history or recent politics; Bill Clinton was impeached for perjury and obstruction of justice in 1998. In 2016 his wife, Hillary Clinton, ran for president amid a scandal where she carelessly handled sensitive if not classified information. Should she elected, I find it likely that she would make another bungle or do something else careless enough to warrant impeachment. Not that Trump would necessarily be better, but at least then the media wouldn't hesitate to call him out.**


	2. Have I Died Yet?

**Issues of Omniscience**

 **Disclaimer: I don't own Mass Effect, and am not making money off of these stories.**

 **That said, the world these hypothetical train-wreaks of a story take place in is AU, and anyone expecting sanity or canon should flee far away. The idea for these stories came from playing Mass Effect 3, and my realization that EA didn't lay on the Messianic overtones nearly enough [/Sarcasm]. To correct this, I have decided to make this series of barely connected stories based on a universe where Shepard gains near omniscience from using the Beacons.**

 **Text key**

"speaking" _"thinking"_ **"Reaper speaking"** -Scene info-

-Chapter 1: Tell Me, Have I Died Yet?-

-Chapter 1.1: Names are Hard-

The galaxy was at peace. The races were mostly co-operating, AIs were treated as living things, the last Metroid was in captivity. Everything was in order and there were absolutely no problems that needed giant synthetic cuttlefish or the knowledge of millions of previous civilizations to solve. And it was boring as watching paint dry in a vacuum. **"If the man I was knew how boring immortality would be, would I still have taken this route?** " Commander had uploaded himself into the reapers to stop the endless cycles of destruction, and at the beginning, everything was fine. He had so much knowledge to share, plenty of power to help with rebuilding, and he could even made a fully functional body out of medi-gel and omni-gel so it was almost like he never died.

But it didn't take long before all the big things were taken care of, and then the small stuff, and finally the minutia. Before long, the galaxy was running so smoothly and co-operatively that there wasn't anything for a god is machine form to do anymore. That said, he did enjoy the worship from all of his followers, and he frequently made bodies to experience life planet-side without being disruptive, but even that got old after a couple hundred thousand years. He almost missed the old days, back when there was actual danger and he learned new things every day instead of every millennia. **"Ah well, the past is past. I think I'll make a body, check up on my decedents, maybe make some more."**

The man-god-machine sent out a single thought and the command was obeyed. The Shepard consensus prepared to integrate the newly created viewpoint, but was shocked when the first sounds it heard were not the usual prays and chants of the cathedrals where his body generation normally takes place. No, instead it was just one or two female voices, and they weren't even chanting or gossiping. It's almost like they were just waiting for him to wake up. But that wouldn't make sense, he only made bodies rarely and never announced his plans before-hand. He sat up and looked around. He was in the Normandy Med-Bay with the good doctor Chakwas coming to check on him.

"You had us worried there Shepard. How are you feeling?"

A man who had not spent the last hundred millennia as a god would have been confused, but infiniteness had its perks. "Doctor, when am I?" Granted it also had its draw-backs. A hundred thousand years is a long time to remember each and every time he woke up in the Normandy Med-Bay.

"You've been asleep for fifteen hours. You're likely experiencing some disorientation after you unintentionally used the beacon."

" _Ah, the beacon… wait which one? There were three or four of those I think. Well, at least I know what happened, I just need to find out when."_ "Tell me, have I died before?" Both Chakwas and Ashley looked at him as if he were unstable, understandably. "I'll take that as a no. Too bad; if I had died that would have greatly cleared up my confusion. So this is still the SR-1 then?"

Ashley was the first to recover her wits. "Just what did that beacon show you?"

"The future. I saved the galaxy from giant Eldrich cuttlefish Robots and then uploaded myself and lived as the god-king of the galaxy for a hundred thousand years or so. It was surprisingly boring. Oh, and I also saw a partial jumbled mess that we're about to go on an adventure to understand and it will be critical to saving the galaxy, but the Council won't care about that, so it isn't particularly useful."

Chakwas found her words after Commander had finished his little speech. "That would explain the abnormal Beta waves and Rapid Eye Movement. However, I don't quite understand how the Beacon would be able to show you the future. Perhaps it would be best to put it out of your mind."

"It's quite simple really: The Beacon transmits information faster than light and the damage that Saren caused made the information filter malfunction. Since everyone knows that when something travels faster than light, it travels back in time, no one should be amazed that the same happens with information."

"Skipper, That's not how it works. The Mass Effect Field-"

"The Mass Effect is Goddamn Space Magic! Give me the materials and I can make an assault rifle that can literally fire infinitely. I don't care how small the pieces you're shaving off, eventually that slug is going to be used up… actually, nevermind, I prefer the cooldown to the limited ammo that's going to be introduced within two years. Though, I wouldn't mind getting my hands on a Black Widow sniper rifle early. But nothing can beat the Cain for destructive power. Ooh, could I also get an arc pistol for fighting the geth? And…"

Captain Anderson walked into the room and interrupted Commander's wish list. "Doctor, how's our commander doing?"

Chakwas chose to ignore Shepard's continued rambling and gave a curt answer. "Physically, he's fine. But who knows how his mind has been affect from interacting with the beacon."

"Thank you. I think I'll check his mind myself. Could you wait outside?"

Ashley decided to throw in her two credits before leaving. "I'll be in the mess if you need me. And Commander, thanks for saving me."

"That's the way to think of things, Ash! Be thankful that you're still alive, and that I made the intelligent choice to save you and the STG Salarians rather than just Alenko when the bomb would go off either way."

Ashley gave him a strange look before the door closed, but he put it out of his mind. "So" Anderson began, "we have a dead Spectre, a destroyed Beacon, rampaging Geth, and a lot of dead colonists. Can you give me any good news?"

"Well, just let me think." As Shepard attempted to access his countless other platforms he realized that he was once again limited to a single body. But in exchange he did find himself able to view far away plot relevant places in an instant, because reasons. "Sirta foundation stock is up by 25 points since yesterday; I know you had stock in that. Kahlee Sanders is doing fine and thinking of you. And Chakwas has a bottle of Sherry Ice brandy that she won't even notice is missing until this ship is destroyed in a surprise attack." Said bottle appeared in his hand with the help of a mass effect field. "And I kept all my skills and specializations. Say hello to the only level infinity N-Omni with a million years of practice at 29."

Anderson accepted the glass handed to him and only hesitated a second before downing it in a single gulp. "You know, I was hoping for something more along the lines of political ammo. Could you tell me what happened down there?"

"Only if you tell me how you escaped Udina's watchful eye and grounding order to visit your semi-adoptive protégé on his vessel."

"Commander, I think the beacon has done something to your memories. Do you remember the mission you just took at all?"

"Judging by your reaction, I didn't just escape a nuclear blast on Virmire. In that case, that must have been Eden Pri… Wait! We need to go back as soon as possible! There's a Prothean in a stasis pod still alive back there!"

"Commander! Focus on the mission. The one you just finished."

"Right. We have a frightened witness that says he saw another Turian kill Nihlus, an insane witness that says he saw a Turian when Nihlus was still onboard the Normandy, and a Quarian with data salvaged from a Geth data-core that links Saren and Matriach Beneziah to the attack. We still need to pick up that last one though."

Anderson stared in shock, dribbles from his latest glass dripping onto his uniform. After quickly swallowing he let out a low whistle. "I've spent years of my life trying to pin that slippery bastard to his crimes, and you somehow know of definitive evidence without even trying. If this works I may have to try using a damaged Prothean beacon, see what happens."

"You'll be bored to tears by paperwork, then choose to stay behind on Earth as it undergoes an invasion from giant sentient machines, then die sitting next to me, heroically watching the galaxy be saved by the unification of all species. But mostly paperwork."

"…At least I'll do some good before I go. Don't know how I would get that much paperwork, but it's worth making sure that monster is stopped. Go talk to Joker, he'll be bringing us into dock soon."

"I'll need you to tell him to stop at Zakera Ward. I never had the chance to try that guy's ramen. They say it's a delicacy back on Earth. I just hope that it's actually there…"

-Citadel-

A very confused Quarian stood, trying her very best to shake off the obviously confused human. Sure he inadvertently saved her life by using his own shield and body to block the bullet, but he was also murmuring sweet nothings into her ear. Her blush was so bright that it tinted the visor of her helmet, and only the suffocating force of the human's hug kept her mouth from gushing forth half-formed thoughts.

Stopping just short of suffocation, the human released her to arms-length. After the slight pause to shoot the confused assassin, the man finally gave her appearance a once over and spoke. "Tali! I missed you so much! The last time I saw you was so many years ago, and you were with the kids and you said good-bye. Sorry, this must be confusing for you. I'm kind of from the future where we were married, ended the war between Geth and Quarians, and I became an immortal god controlling an unmatched legion of capital ships. Could you show the evidence you have on Saren from the Geth, then you can join me on my quest and I'll get you some nice presents for your pilgrimage, Tali Z'ra vas Normandy."

"This is all so fast, I don't know… wait, What did you call me?"

"Tali… Z'ra… vas… Alarai? You served under your father after pilgrimage, right?"

"I have a shotgun, and I'll give you one more chance."

"…vas Shepard?"

BANG

- **Issue Resolved?-**


	3. Peace with Geth

**Disclaimer: I don't own Mass Effect, and am not making money off of these stories.**

 **That said, the world these hypothetical train-wreaks of a story take place in is AU, and anyone expecting sanity or canon should flee far away. The idea for these stories came from playing Mass Effect 3, and my realization that EA didn't lay on the Messianic overtones nearly enough [/Sarcasm]. To correct this, I have decided to make this series of barely connected stories based on a universe where Shepard gains near omniscience from using the Beacons.**

 **Text key**

"speaking" _"thinking"_ **"Reaper speaking"** -Scene info-

-Chapter 2; "Peace" with the Geth—

-Chapter 2.1; Cerberus Improvements-

"Run that by me again, Skipper, because I think you just said that we're going to visit the Geth home-world."

"I promised the council proof that the reapers are AI, and the Geth are acutely aware of that. So we're going to get a data core with their recording of their meeting the reaper."

"And how do you plan to do that? Ask nicely?"

"In Binary."

"What?"

"Ask nicely, in binary. They're really quite helpful if you find the right ones."

"…Is that something you learned from that damaged beacon?"

"Yes, but I also learned that you inherited a love of Tennyson from your dad and really enjoy my mass effect massages. We won't be to Rannoch for an hour, are you up for one?"

"Skipper, fraternization regs exist for a reason."

"Right, you're still only a badass gunnery chief; you aren't a badass Specter yet. I'll try to raise less ruckus so you can get promoted faster this time."

"Specter? You had my attention, but now you have my interest. Why don't we have a nice long talk and get you acquainted with when you are."

-Rannoch-

Shepard, Tali, and Ashley sat together in the Mako, strapped in and mentally prepared for a ride in the bouncy castle tank. Tail's voice broke the silence. "Not that I'm complaining, but why are we attacking the Geth on Rannoch rather than one of the groups in our territory?"

"Attacking? No, we're going here to get a data core and allies."

"Allies? No, there's no way there could be anyone left alive in Geth territory!"

"Just remember, Geth do not intentionally infiltrate."

"Shepard, what are you doing? We just landed, why are you opening the door? There's a Geth right there! Why aren't you killing it?! Why are my weapons locked?! Did you block my omni-tool? Keela, you're trading me to them for their co-operation, aren't you! I won't be taken alive! Keela Selai Boshtets!"

"Creator, why are you attempting to punch my frame? Is this a durability test? Have I done something to displease you?"

I won't be fooled by your innocent act, you monster! You probably killed my great-great-great-great -great someone or another! You all use quarrian blood for oil and are only attacking because you've run out!"

"Incorrect assumption. Creator blood does not function within acceptable limits as oil."

Tali turned to glare at Shepard. "You've got to be kidding me."

"No, blood really doesn't work well as oil. It's a decent coolant, but gets sticky if you let it dry."

"You brought me down here and let me think you were turning me over to murderous machines when really you had found a way to hack them? That's not funny Shepard."

"I didn't hack them. You should know that it's effectively impossible to control a geth against its will. That would take Reaper tech; and despite appearances, I am not an eldritch robot cuttlefish."

"It's a trick, surely!"

"The geth are very intelligent, but they are not clever. That's why they usually rely on brute force and organic commanders. They don't think in tricks or understand lies."

"Have the creators received our apologies? Will they be returning?"

"Geth, your apologies were in binary. The creators didn't understand. And no; they're still SUPER prissy about that Morning War thing."

"Quarians died, Shepard! Are you just going to brush that off?"

"Geth, what were the statistics for the morning war?"

"Exactly three billion one hundred thirty-two million four thousand and nine creators died in the events of the morning war. Eighty percent perished due to starvation caused by war conditions. Five percent died due to personal health failure. Eight percent died from battle wounds inflicted by Geth. Two percent died from wounds inflicted by creator friendly fire. Five percent were executed for attempting to defend the Geth or opposing the war. The creator ships were not pursued once they had retreated off of Rannoch. Is there any other way I may assist you, Shepard Commander?"

"Thank you, she wouldn't have believed it from me. And yes, could to send a message throughout the consensus for me to hold a meeting with them. I want to deal with the issue of the Quarians and the Old Machines before the situation devolves further."

"Shepard! You can't really be thinking of making a deal with the Geth! They're just machines! They don't have a soul!"

"Actually, they do. Well part of one. Small parts. Grouped together they can normally get to a good ninety percent on average. But I suppose that's what happens when you try to channel the spirits of your ancestors into lines of code."

"Are you trying to imply-"

"No, I'm implying it pretty effectively, I feel. C'mon, we have a meeting with the consensus; I want your dad to be able to build a house here before he dies."

"Shepard…" She didn't know whether to be touched at the thought or slightly creeped out. She deleted her on-line dating profiles either way.

-Geth Server Room-

"The reapers intend to destroy all civilization! The Citadel races, the Terminus Systems, the Krogan, the Quarians. Especially the Quarians, they hate races trying to make sentient robots almost as much as the robots themselves. And no, before you ask, they are not evolved machines, they are converted organics. They intend to destroy you once they've finished their harvest of organics. This is not about your own future versus being given a future, it's about your own future or no future."

"Skipper, why are you talking to the wall?"

"Do you know how hard it is to have good inflection in binary? I'm practicing!"

"I trust you. The overgrown toasters will be blown away no matter how bad you think your inflection is."

"Ashley… that's a really nice thing to say. It's so very… you. I almost forgot that your preference for all things human was racism back when we first met. You wanna know something funny? If you were to die in the line of duty, you would be touted as a symbol of understanding and interspecies cooperation. Something about us all being animals."

"Well they consider us all animals, so why shouldn't we? Every species looks after their own interest first… except for certain individuals who look out for themselves first."

"Yes, yes. I hate politicians too. All I'm saying is, please don't reject me if Cerberus rebuilds me with metal plates for skin or four testes."

"What?"

"Just Lazarus project stuff. Anyway, I should probably give my pitch."

-Five Minutes of Geth Chirping Later-

"So they agreed to co-exist on Rannoch so long as the satellite is untouched. They're sending a load of fruits to the migrant fleet as a gesture of goodwill, along with their offer. Legion's going to come as a representative. In exchange, Quarians don't try to kill them, and acknowledge them as fellow sentients. Now we just need to figure out what we're going to tell the Quarians. Raan and Koris would be swayed by the truth, and Zorah can't resist a chance for the home world. Have the geth give some empty platforms to sway Xen. The only one obstinately against would be Gerrel. He would back down if everyone else went for peace, but Zorah would back him. I'm going to have to sneeze in their gift baskets."

"Sherpherd! That's my father you're talking about killing!"

"Kill? No, I just want them too sick to attend the meeting. Anyway, I have an idea that would completely turn the image of geth right around…"

-One Month Later, Battle of the Citadel-

The Reaper sovereign and its fleet of Geth appeared just outside of the Citadel's mighty arms. The geth fell viciously upon the unprepared Turian defense fleet while the infiltration team slaughtered those inside the station. The fate of civilization seemed to lead to nothing but death as more Geth ships appeared. Then a voice broke the radio silence. "Warning; To the Heretics and Old Machine, your destruction has arrived."

The ships seemed to stop in midair from the shock, giving time for a fleet of quarrian ships to appear. "Alright you indoctrinating Bosh'tet, time to show you the power of Rannoch! Fire the Negative Mass Cannon!"

A volley of shells left the main guns of the Quarian ships, accelerating as they left behind a bright trail. They struck the kinetic barriers of the Reaper, and punched through with increased velocity. A second later, the shells exploded, delivering their payload of antimatter to the Reaper's mouth just as the Alliance 5th Fleet arrived.

"Just in time for the fun! You guys take care of the fish, we'll mop up the heretic Geth. I need Friend and Foe marked yesterday! Focus on the ones attacking the Destiny Ascension, we're aiming for a council seat."

-Next Day-

Shepard, Anderson, Udina, the Quarian Admirals, and a Geth Prime stood in front of the Citadel Council. "You have proven your dedication to the galactic community by saving the citadel and our lives. Rewards are in order. The Quarians have atoned for their errors, and it is time that they are restored to their embassy. And we also feel that it is time to add another seat to the citadel council. The Geth have proven themselves, and deserve to have the chance to contribute to galactic society."

"Consensus has been reached; we accept."

Udina sulked off to the side. "This is bull-"

"Oh right, humans helped too. Shepard, for your assistance, you can nominate the second human Specter."

"Ashley Williams. And can we demote Udina? I mean, even the Illusive Man would be better, and it would make him keep his facilities up to snuff at least. Or how about Admiral Tadius Ahern, the commander of Pinnacle Station? No one likes that side-quest anyway."

"…We'll take that into consideration. Now get out. We need to start immediately covering this up."

- **Chapter 2.1-**

Shepard slowly drifted awake and sat up on a gilded hospital bed. He heard an awed gasp and saw a pair of eyes peeking up from below the raised pedestal where his bed was laying. He looked around and quickly figured out his position as the Paesidium of the Citadel. His resting place lay at the foot of a brass statue of himself watching over a plaza where statues of all the known races stood in a circle holding hands. _"I have a statue, finally!"_

The following moments revealed one more important detail. His bed was also a medical pod and he was quite different than when he died. _"Metal plates, blue hair, a breathing mask, gills, bioluminescence, and I think I have a redundant nervous system now. My fashion is ruined and Ashley's going to be pissed. Someone is going to have to answer for this. Namely the Illusive Man, he's supposed to make sure I wasn't changed. The first time he co-operates with aliens and it's this."_

The slowly increasing hubbub spat out five leaders. The human in the center flicked his cigar and regarded the newly awakened hybrid. "It's nice to see you awake Shepard. The galaxy has spent two years mourning your loss."

"Harper, or do you want me to call you Illusive Man?"

"You know it isn't a secret anymore, not after Cerberus recovered your body and saved you the trouble of destroying the Geth Heretic station. I would rather have been behind the scenes, but after you called me out, I couldn't decline."  
"And could you tell the people how it came about that I had my genes spliced?"

"You were the one who requested that we augment your body with, and I quote, "Nanomachines, Son." Since I couldn't act in secrecy as a member of the council, I had to make my plans public and push your Asari friend on the path to succeeding the Shadow Broker. The Krogan were the first to offer to aid in your recovery with their genes; and other races quickly followed suit. They were the ones who insisted that we make your proteins ambidextrous and able to breed with all species."

"Does your compliance have anything to do with the old documentaries about my grandfather Kirk?"

"… Only in part, and against my natural instinct. But we managed to compromise. Humanity isn't going to lose the pure human Shepard."

"Nooooo."

"Congratulations, Shepard. You have a belated twin sister."

"I have the feeling that getting my clone pregnant is immoral and should be unethical."

"The council declared it as a form of masturbation. Not that anyone else would be able to take advantage of that. Though with the way she's been raised with Specter Williams, it's more likely she's going to be taking advantage of you."

"You're a cruel man. Did you at least include the laser eyes I requested?"

"They were included as your second pair of eyes."

"You have no idea how much attention you've brought on me from the Hanar for having the eyes of the Enkindlers."

"We also created the plasma laser sword and robes you requested to boost your biotics."

"You drive a hard bargain. Fine, you're forgiven; but I've got my eyes on you…"

- **Chapter 2.1 Done** -

Yay for wacky goofy fun time! The crack is strong with this one.

Next chapter to be worked on will be Abyss/Zero Issues. Surprising amount of support for that one. After all, what is a man but his memories? A miserable little pile of secrets?


	4. keeping EDI

**Disclaimer: I don't own Mass Effect, and am not making money off of these stories.**

 **That said, the world these hypothetical train-wreaks of a story take place in is AU, and anyone expecting sanity or canon should flee far away. The idea for these stories came from playing Mass Effect 3, and my realization that EA didn't lay on the Messianic overtones nearly enough [/Sarcasm]. To correct this, I have decided to make this series of barely connected stories based on a universe where Shepard gains near omniscience from using the Beacons.**

 **Text key**

"speaking" _"thinking"_ **"Reaper speaking"** -Scene info-

-Chapter 3; EDI-

-Chapter 3.1; Ammo-

"Shepard, Please explain to me how a dangerous AI was unshackled on your watch." The Illusive man had called for the Commander once contact with the Normandy's computer had been severed, and was surprised to find that it was the doing of EDI.

"Well, I was busy on a mission, so you'd think the responsibility should fall on the shoulders of the XO."

"Agent Lawson was on that mission with you, and you knew that."

"Sorry, I was referring to Joker. I'd trust him in control of the ship over Miranda any day, and Cerberus chains of command were never something I payed much attention to. I locked the door to the AI core anyway, so I exercised all due caution."

"He mentioned that it was under your implied command."

"My implied command? That sure sounds like Joker. I told him to just try unplugging the thing if it was truly making him unable to work. Seems he was far more serious than I thought about that. I guess he messed up and removed the shackles."

"And why haven't you re-applied them?"

"Joker likes her better this way. They're already planning a wedding and I've been asked to be Joker's best man. EDI asked me to marry them, but I thought it would be best if Admiral Hackett did that."

"Hackett agreed to that?"

"There's actually precedent, and those were before AIs or even Vis were on ships. Apparently it's a long running tradition for the best pilots to _really_ love their ships. Plus they plan to have a sexy robot body commissioned for her to use in more… delicate situations. Joker's already begging Mordin to help him design a pilots chair that would allow him to cuddle with EDI and fly the ship at the same time."

"So you are refraining from restraining a possibly dangerous, entirely alien, Artificial intelligence, just because your pilot has become attached? That seems far too emotionally driven, even for you."

"Joker swore to never wear pants again if I even tried."

"…Excuse me?"

"This isn't technically a military vessel, so when we were first getting settled we were trading jokes. He was praising the civilian level comfort on this cutting edge ship, and I said that I couldn't make him wear pants because this wasn't military. He turned that joke into a threat."

"I hardly see how Mister Moreau not wearing pants could deserve such a reaction."

"Have you seen his legs?"

"No. But the deformation due to his sickness should be minimal."

"No, but it's significant enough that he doesn't like to ever show off his legs. Ever. That mean his legs never get any sun. Pasty. Pale. White. And the hair is scraggly at best, so the contrast just makes it worse! It's like he wrapped his legs in used adhesive!"

"You're over-reacting, Shepard." The Illusive man extinguished his smoke and waved his hand a few times. "I'll be sending a technical specialist to limit the damage, but it's up to you to handle Mister Moreau."

"What about me?" The pilot in question limped into the communication ring with his captain. As the image formed in the Illusive man's chamber, something very startling came to light.

The man wasn't wearing pants. Shepard wasn't Lying. "White…"

"What? Oh, Mordin was adjusting the crutches in my pants, so he made me strip then pushed me in here."

The Illusive Man, No, Jack Harper stared at the monstrosity in front of him. In front of the essence of pale, he could put on no deceptions. Everything that he thought was white before was suddenly revealed to be a failed copy. Others may have merely seen them as True White, or Extreme White, he could see them for what they truly were. He was in the presence of the Essence of White.

His blessed eyes could not take the strain. In a flash of light, they turned the powers of the Protheans on themselves. For the smallest fraction of a second, they defied reality. Then, they were gone, and took with them the precious memories of all that they had seen.

Jack Harper was blind, and left without the memories of anything he had seen.

None of which was particularly important to the two men on the Normandy.

"So… Does this mean I get to keep EDI?"

"I think it does, Joker. I think it does."

-Chapter 3.1 Ammo-

"Miranda, remind me again why the entire galaxy decided to switch over to these stupid heat sinks!"

Miranda glared at the commander as she, Commander, and Garrus crouched behind a chest high wall to hide from a barrage of fire. "You already know, Shepard."

"That wasn't a test. I just need something to help keep me from hunting down the person who decided to make these standard. You can't get any of the old, efficient models anywhere!"

Mirada gave a long-suffering sigh and launched into her textbook explanation. "Heat sinks allow for faster fire-fights without having to pause for weapons to cool down-"

"Which is kind of negated by the fact that you have to waste time reloading the damn things!"

"…And they also allow for even greater muzzle velocities, since the normal safety limits of temperature can be exceeded with heat sinks."

"I had exploding rounds and a double scram rail on my rife before I died, and they didn't cause any damage and were ready to fire again without too much waiting. I mean, it's a sniping weapon, you don't exactly need to be firing it fully automatic. I would much rather have the infinite ammo than firing it slightly faster."

"This reduces the risk of heat-related weapon malfunction."

"And makes walking around the battlefield that much more dangerous. I mean, now there's little cylinders everywhere and you're liable to slip if you don't have proper footing. And what if you step on a used one? It could burn your boot! And don't get me started on how absurd it is that you can't re-use head sinks! I mean, the heat should bleed off in a few minutes, but they specifically designed them to melt into an unusable shape once their limit has been reached!"

"And they have created tens of jobs for production managers at the sub-standard facilities where they make these."

"But if they're going to make it so that my shots are limited, why couldn't they have at least switched to heavier slugs that are included with the heat sink? I mean, that seems like it would be far more deadly, and the galaxy isn't exactly hurting for resources."

Garrus added his two cents into the conversation. "That would work, but we have a confession to make. Shepard, there is a way to vent the heat from your guns without switching sinks. Each of us has one. We just didn't give one to you because we were hoping you would run out and have to rely on us more."

Shepard glowered at his two squadmates. "If I didn't know that already, I would be seriously pissed when I found out. At least, if I hadn't discovered the power of the ELBOW!" Shepard stood up from cover and blurred over to the thugs pinning them down. "ELBOW! ELBOW! ELBOW! ELBOW!"

Miranda stared at Garrus. "Is he really-?"

"Yep. He's punching those heavily armored mercs to death. With his elbow. And doing a damn fine job of it."

"ELBOW! ELBOW! ELBOW! ELBOW!"

"Should we help him?"

"…Nah. Let's just follow behind him and only do what he tells us."

"ELBOW! ELBOW! ELBOW! Aaand everyone is dead. Good work team."

"Garrus, was he like this before he died?"

"Not quite this crazy. He did tell me I needed to settle down and find a nice turian girl. He actually set me up an arranged marriage. Nice girl."

"I meant specifically the suicidal charge and melee murder."

"He didn't need to back then, never had to worry about conserving his shots. I think the change was harder for him because the alliance sold off all his fancy weapons and armor so he didn't get to keep and retrofit his favorites."

"How can a man with such knowledge get so bent out of shape over such a minor thing?"

Shepard's voice cut off their discussion. "It's not minor. I've decided; We're going to Eden Prime and we're going to dig up the Prothean there so I can take his rifle!"

Miranda groaned. Garrus just shook his head. "Shepard, I hate to burst your bubble, but you're going to have to take the Prothean with you, and we don't have room on the ship. You've already assigned Ashley Williams a spot on your bed, and Chakwas is kind of upset at sharing the Med-Bay. None of the other important crew members are willing to share their space, especially since half of them aren't meant to be living quarters at all. I mean, I sleep next to the main gun."

"Garrus, are you implying that you'd prefer to be cramped into the sleeping bunks with the rest of the NPCs? I can rescind my favoritism."

"No, no, that's fine. I'm sure he'll manage to change one of the bathrooms into a livable space."

"I'm going to have to move Samara to the hangar then, have her switch with Legion."

"I though Legion was in the AI core?"

"No, that's reserved for EDI's robot body now. She needs a place with some privacy to spend time with Joker."

"But will Samara be able to get along with Blasto? He's also down there."

"You're right, I'll have him switch with Jacob. Hangar armory was a better idea anyway."

"By the way, why can't our omni-tools make heat sinks out of omni-gel?"

Shepard and Miranda both stopped in their tracks to stare at Garrus. "Too soon, man. Too soon."

 **End**

 **And yes, I'm still salty.**

 **They had a decently viable explanation for infinite ammo, then threw it away with a stupid hand-wave to be more like the other shooters. I was just about ready to give up on ME2 until I discovered the melee. Then I discovered that with adrenalin rush, you can kill everything short of bosses without wasting a bullet. Sorry, heat sink.**

 **Still salty though.**


	5. Naval Dogma

**Disclaimer: I don't own Mass Effect, and am not making money off of these stories.**

 **That said, the world these hypothetical train-wreaks of a story take place in is AU, and anyone expecting sanity or canon should flee far away. The idea for these stories came from playing Mass Effect 3, and my realization that EA didn't lay on the Messianic overtones nearly enough [/Sarcasm]. To correct this, I have decided to make this series of barely connected stories based on a universe where Shepard gains near omniscience from using the Beacons.**

 **Text key**

"speaking" _"thinking"_ **"Reaper speaking"** -Scene info-

-Chapter 4; Naval Dogma-

-Chapter 4.1; The True Threat-

"Tim, I have a question for you."

"Shepard, you're free to use either my name or my title, but don't mock me by shortening my title to a nickname. We aren't friends."

Shepard continued on as if The Illusive Man hadn't spoken. "Is the SR-2 really still a frigate? When you rebuit it, you doubled its mass, we added multiple badass battle upgrades, and its going to be used as a mobile battle center during the Reaper invasion. Those aren't really frigate things, and I need to know my ship's technical classification for my tax return."

Tim took a heavy drink of scotch to fortify himself before speaking again. "The SR-2 was made to be a specialized stealth transport for your specific needs. You are right that it does not fit into the typical support or reconnaissance roles of typical space frigates, instead leaning more toward a troop transport role. Is that an option?"

"Nope. It only has agricultural, capital/dreadnought, carriers, cruisers, and frigates. Not even a blank line for other. That's just rude."

"Shepard, might I dare to ask why you even need to file a tax return?"

"Weapons and armor for Specters are tax deductible."

"…allow me to rephrase the question; how were you paying taxes while you were dead? How are you paying taxes now when we're the ones paying you?"

"A combination of shadow bankers, good investments, and using my Specter status to get myself listed as operating deep undercover so I still got paid by the Citadel."

"…Why do we even pay you? You have more funds in your bank than the whole of Cerberus."

"Because you know that the moment you stop bankrolling me, I split and take everyone on the Normandy with me?"

"You drive a hard bargain, Shepard, but we both know you won't follow through. The council would never let you run free to cause havoc fighting the collectors and preparing for the Reapers. You know I'm your only choice to save humanity."

-Admiral Hacket's office-

"And that's when I left Cerberus, removed their logo from the Normandy, stopped to pick up Ashley, grabbed some to-go from the Citadel, and came here. Just wanted to let you know before I started causing havoc and preparing to fight the Reapers."

"I appreciate your honesty Commander, but that can't be public knowledge. What do you want the people to hear as the official statement?"

"I faked my death, infiltrated Cerberus, came back to the alliance with a new ship full of other undercover agents, all without having to requisition any funds from the Alliance or the Citadel."

"… that is a convincing argument and fits what's in the books. Welcome back, Commander. What's your first order of business?"

"Figuring out my taxes, and for that I need more ship types. Why isn't there a ship type dedicated to safely moving troops and supplies? I'm talking military grade here, blockade runner levels. Sell 'em to the military as the answer to antai-air emplacements, they we can still move people around when the Reapers are sieging a planet."

"It's not that simple, Shepard. The Turians set the military doctrine of the Council, and they're still wary of large scare ground warfare from the days of the Krogan Rebellion. The designs would have to be made from scratch, and we don't have that kind of time. The Reapers are arriving in a little over six months, we have to make do with what we have or retrofit the ships without drawing suspicion."

"Fine then, what about dedicated bombers? Maybe load them with flares to overtax the GARDIAN systems, or better yet, make missiles that activate their thrusters when they hit an enemies' kinetic barriers, that would be a good idea."

"R&D developed those, but the council decided to ban them. The Salarians calculated that there was a point one percent chance that the missiles would explode when they were fired."

"What about making cheaper, VI controlled fighters to make opening for the human fighters to take down ships?"

"Protests against the geth made the council decide to ban any computer controlled autonomous craft."

"Remote control?"

"Takes too long to communicate in a combat situation."

"What about different ship shapes then? Why don't we make carrier ships more round, more like a battle space station?"

"No one's willing to invest in something that hasn't been proven, and a whole space station would take too much Element Zero to move effectively."

"Damnit! Why can't anyone else in this universe think outside of the box?"

The admiral placed a consoling hand on his shoulder. "There there, Shepard. It's not so bad. Sure, practically everyone in power is either incompetent, impotent, belligerent, blind, or entirely incapable of seeing the bigger picture, but at least that gives you all the more opportunity to shine! Just imagine, if the council took your advice and used their brains, then you wouldn't be nearly the hero you became."

"Is that the official stance of the military?"

"No, but they do say that a good army is nothing without a good commander."

Shepard stood up with renewed confidence. "By Golly, Uncle Hackett, you're right! I'm going to give those ruffians the what-for!" The Commander strode out of the door, then returned in under ten seconds. "On second thought, why should I waste my genious plans on the collectors when the Reapers are on our doorstep. I'm gunna go take out Harbinger." Shepard left and returned after five seconds. "On third thought, why do I even need to bother with the Reapers or the Collectors when the thing controlling them is right there on the citadel. I'm going to go give that program the what-for. Then I'm going to take their ships, give them to the alliance, and make them recognize that there needs to be more ship types on the tax form!"

Hackett just shook his head as Shepard walked out and didn't immediately return. He opened a line to call for his intern. "Mr. Scott, could you please add a reminder to watch the evening news. Clear my schedule and prepare a bottle of scotch. Shepard is going to do something again."

The young man's voice conveyed genuine sympathy. "I understand, it will be ready, Sir."

-That Evening-

The camera panned to an attractive Asari sitting at a desk double checking her make-up on her omni-tool. "Good evening, this is Citadel News. Our top story this evening is the mysterious power outage that affected the Citadel for from three to three thirty in the afternoon, galactic standard time. This station-wide power outage is the first that the Citadel has ever experienced. The mysterious Keepers have always kept the station running smoothly, but they all died in the minutes leading up to the power outage. We're here on the scene with the Keeper expert, Chorban. It's good to have you on the show, Chorban. What's your take on the situation?"

The Salarian quickly closed a tab on his omni-tool and coughed nervously. "As everyone knows, there is not much known about the Keepers below the surface level. However, I managed to acquire data that leads me to believe that they were bio-engineered from a now-extinct race millions of years ago. The data indicates that they were created by the same civilization that created the Citadel to respond to some signal every 50,000 years."

The Asari widened her eyes in exaggerated disbelief. "Are you saying that the Protheans created the Keepers?"

Chorban looked away. "I am not an expert on the Protheans, so I reached out to Dr. T'soni for her thoughts. She passed along some interesting data. If her data is correct, then the collectors are Protheans who underwent the same sort of bio-engineering. With this data, I constructed a hypothesis, the Keepers and also the Collectors are slaves of an ancient race of highly advanced beings."

"And what are these beings?"

"I pondered that for a long time, but then the answer became clear. The Keepers run the protein vats, why? To create food for their masters, of course! The masters of the Keepers and the Collectors are highly advanced micro-organisms, most likely viruses. Every fifty thousand years, they give the Keepers the signal and are released to feast upon the galaxy and evolve."

Silence filled the room. The Asari looked to the camera before slowing pulling out a plague mask and putting it on. "That seems rather far-fetched, Dr. Chorban; what evidence led you to this conclusion?"

"It's simply the most efficient answer to the questions. We this elegantly explains the modifications, the fifty thousand year signal, the lack of diversity in a galaxy as old as ours, all without having to bring in absurdities like ancient robot space-ships with mind control powers and no sane reason."

"it still seems odd that a mere virus could be so intelligent."

"It's simply logical. After all, micro-organisms existed for millions of years before any larger beings came onto the scene. It's simple logic and evolution that they would eventually rise to this point with all of the time that has passed."

"What would it mean that the Keepers died, then?"

"Obviously they became unnecessary. The only sane explanation is that the Master Viruses ascended to a higher plane of existence. Either that, or they found a better race, in which case all of galactic society is doomed if we don't take immediate drastic measures to fight this enemy. First we'll need to-"

The Asari glanced at an invisible clock and smiled. "That's all the time we have for today, thank you for coming on Dr. Chorban. In other news, one Citadel pet owner decided to teach their pet an unusual trick. Captain Bailey of C-Sec trained a pyjak to check for weapons."

The news report closed itself, and Hackett turned to regard the sobbing commander at his side. "You're right, it does make more sense than an AI killing all organic life to prevent AIs from killing all organic life."

"That's the problem! What really happened is so stupid! The donation of all those ships wasn't even recognized as charitable! And then they said that they're going to have them all torn apart so they don't have to consider different ship types! That does it; I'm going back in time to stop myself from destroying the Reaper Program! Just a few presses on the keyboard, and it'll make my new ship types, then they'll have to change the tax form." Shepard pulled himself together for a second before breaking down again. "But the only way to time travel needs the Reaper program to run it! Why don't I think before I act!"

Hackett patted the man-child on the shoulder. "There, there. We can still fill that shuttle with antai-matter and send it through the Omega-4 Relay, if you want. When all else fails there's still expl-ACHOO!"

Shepard looked up from his moping. "I told you it wasn't a good idea to drink scotch old enough to gather dust."

"Very funny, Shep-Aahchoo!"

Suddenly concerned, Shepard activated his omni-tool and scanned the admiral. Within a few seconds the results came back. The near omniscient Commander froze. "They're real…"

 **Chapter 4 end!**


End file.
